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Wei W, Li S, Zhang Y, Deng S, He Q, Zhao X, Xu Y, Yu L, Ye J, Zhao W, Jiang Z. Analytical validation of the DropXpert S6 system for diagnosis of chronic myelocytic leukemia. LAB ON A CHIP 2024; 24:3080-3092. [PMID: 38747247 DOI: 10.1039/d4lc00175c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2024]
Abstract
Digital PCR is a powerful method for absolute nucleic acid quantification and is widely used in the absolute quantification of viral copy numbers, tumor marker detection, and prenatal diagnosis. However, for most of the existing droplet-based dPCR systems, the droplet generation, PCR reaction, and droplet detection are performed separately using different instruments. Making digital PCR both easy to use and practical by integrating the qPCR workflow into a superior all-in-one walkaway solution is one of the core ideas. A new innovative and integrated digital droplet PCR platform was developed that utilizes cutting-edge microfluidics to integrate dPCR workflows onto a single consumable chip. This makes previously complex workflows fast and simple; the whole process of droplet generation, PCR amplification, and droplet detection is completed on one chip, which meets the clinical requirement of "sample in, result out". It provides high multiplexing capabilities and strong sensitivity while all measurements were within the 95% confidence interval. This study is the first validation of the DropXpert S6 system and focuses primarily on verifying its reliability, repeatability, and consistency. In addition, the accuracy, detection limit, linearity, and precision of the system were evaluated after sample collection. Among them, the accuracy assessment by calculating the absolute bias of each target gene yielded a range from -0.1 to 0.08, all within ±0.5 logarithmic orders of magnitude; the LOB for the assay was set at 0, and the LoD value calculated using probit curves is MR4.7 (0.002%); the linearity evaluation showed that the R2 value of the BCR-ABL was 0.9996, and the R2 value of the ABL metrics calculated using the ERM standard was 0.9999; and the precision evaluation showed that all samples had a CV of less than 4% for intra-day, inter-day, and inter-instrument variation. The CV of inter-batch variation was less than 7%. The total CV was less than 5%. The results of the study demonstrate that dd-PCR can be applied to molecular detection and the clinical evaluation of CML patients and provide more precise personal treatment guidance, and its reproducibility predicts the future development of a wide range of clinical applications.
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Affiliation(s)
- Wenjia Wei
- Xiangya Hospital Central South University Department of Hematology Changsha, Hunan, China.
- Xiangya Hospital Central South University National Clinical Research Center for Geriatric Disorders Changsha, Hunan, China
- Hunan Hematology Oncology Clinical Medical Research Center Changsha, Hunan, China
| | - Shujun Li
- Xiangya Hospital Central South University Department of Hematology Changsha, Hunan, China.
- Xiangya Hospital Central South University National Clinical Research Center for Geriatric Disorders Changsha, Hunan, China
- Hunan Hematology Oncology Clinical Medical Research Center Changsha, Hunan, China
| | - Ying Zhang
- Xiangya Hospital Central South University Department of Hematology Changsha, Hunan, China.
- Xiangya Hospital Central South University National Clinical Research Center for Geriatric Disorders Changsha, Hunan, China
- Hunan Hematology Oncology Clinical Medical Research Center Changsha, Hunan, China
| | - Simin Deng
- Xiangya Hospital Central South University Department of Hematology Changsha, Hunan, China.
- Xiangya Hospital Central South University National Clinical Research Center for Geriatric Disorders Changsha, Hunan, China
- Hunan Hematology Oncology Clinical Medical Research Center Changsha, Hunan, China
| | - Qun He
- Xiangya Hospital Central South University Department of Hematology Changsha, Hunan, China.
- Xiangya Hospital Central South University National Clinical Research Center for Geriatric Disorders Changsha, Hunan, China
- Hunan Hematology Oncology Clinical Medical Research Center Changsha, Hunan, China
| | - Xielan Zhao
- Xiangya Hospital Central South University Department of Hematology Changsha, Hunan, China.
- Xiangya Hospital Central South University National Clinical Research Center for Geriatric Disorders Changsha, Hunan, China
- Hunan Hematology Oncology Clinical Medical Research Center Changsha, Hunan, China
| | - Yajing Xu
- Xiangya Hospital Central South University Department of Hematology Changsha, Hunan, China.
- Xiangya Hospital Central South University National Clinical Research Center for Geriatric Disorders Changsha, Hunan, China
- Hunan Hematology Oncology Clinical Medical Research Center Changsha, Hunan, China
| | - Linfen Yu
- Shenzhen Biorain Technology Co., Ltd, Shenzhen, Guangdong, China
| | - Junwei Ye
- Shenzhen Biorain Technology Co., Ltd, Shenzhen, Guangdong, China
| | - Weiwei Zhao
- Rehabilitation Medical Center of Jiangning Hospital, Nanjing, Jiangsu, China
| | - Zhiping Jiang
- Xiangya Hospital Central South University Department of Hematology Changsha, Hunan, China.
- Xiangya Hospital Central South University National Clinical Research Center for Geriatric Disorders Changsha, Hunan, China
- Hunan Hematology Oncology Clinical Medical Research Center Changsha, Hunan, China
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Peng K, Wu Z, Feng Z, Deng R, Ma X, Fan B, Liu H, Tang Z, Zhao Z, Li Y. A highly integrated digital PCR system with on-chip heating for accurate DNA quantitative analysis. Biosens Bioelectron 2024; 253:116167. [PMID: 38422813 DOI: 10.1016/j.bios.2024.116167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 02/21/2024] [Accepted: 02/22/2024] [Indexed: 03/02/2024]
Abstract
Digital polymerase chain reaction (dPCR) is extensively used for highly sensitive disease diagnosis due to its single-molecule detection ability. However, current dPCR systems require intricate DNA sample distribution, rely on cumbersome external heaters, and exhibit sluggish thermal cycling, hampering efficiency and speed of the dPCR process. Herein, we presented the development of a microwell array based dPCR system featuring an integrated self-heating dPCR chip. By utilizing hydrodynamic and electrothermal simulations, the chip's structure is optimized, resulting in improved partitioning within microwells and uniform thermal distribution. Through strategic hydrophilic/hydrophobic modifications on the chip's surface, we effectively secured the compartmentalization of sample within the microwells by employing an overlaying oil phase, which renders homogeneity and independence of samples in the microwells. To achieve precise, stable, uniform, and rapid self-heating of the chip, the ITO heating layer and the temperature control algorithm are deliberately designed. With a capacity of 22,500 microwells that can be easily expanded, the system successfully quantified EGFR plasmid solutions, exhibiting a dynamic linear range of 105 and a detection limit of 10 copies per reaction. To further validate its performance, we employed the dPCR platform for quantitative detection of BCR-ABL1 mutation gene fragments, where its performance was compared against the QuantStudio 3D, and the self-heating dPCR system demonstrated similar analytical accuracy to the commercial dPCR system. Notably, the individual chip is produced on a semiconductor manufacturing line, benefiting from mass production capabilities, so the chips are cost-effective and conducive to widespread adoption and accessibility.
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Affiliation(s)
- Kang Peng
- BOE Technology Group Co Ltd., Beijing, 100176, PR China
| | - Zhihong Wu
- BOE Technology Group Co Ltd., Beijing, 100176, PR China
| | - Zhongxin Feng
- Affiliated Hospital of Guizhou Medical University, Guiyang, 550002, Guizhou, PR China
| | - Ruijun Deng
- BOE Technology Group Co Ltd., Beijing, 100176, PR China
| | - Xiangguo Ma
- BOE Technology Group Co Ltd., Beijing, 100176, PR China
| | - Beiyuan Fan
- BOE Technology Group Co Ltd., Beijing, 100176, PR China
| | - Haonan Liu
- BOE Technology Group Co Ltd., Beijing, 100176, PR China
| | - Zhuzhu Tang
- Affiliated Hospital of Guizhou Medical University, Guiyang, 550002, Guizhou, PR China
| | - Zijian Zhao
- BOE Technology Group Co Ltd., Beijing, 100176, PR China.
| | - Yanzhao Li
- BOE Technology Group Co Ltd., Beijing, 100176, PR China.
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Soverini S. Resistance mutations in CML and how we approach them. HEMATOLOGY. AMERICAN SOCIETY OF HEMATOLOGY. EDUCATION PROGRAM 2023; 2023:469-475. [PMID: 38066920 PMCID: PMC10727040 DOI: 10.1182/hematology.2023000447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
Among the variety of resistance mechanisms that may underlie a non-optimal response to tyrosine kinase inhibitor (TKI) therapy in chronic myeloid leukemia patients, secondary point mutations in the BCR::ABL1 kinase domain (KD) represent the only actionable one. Each of the 5 ATP-competitive inhibitors (imatinib, dasatinib, nilotinib, bosutinib, ponatinib) has a well-defined spectrum of resistance mutations. Growing clinical experience will soon allow to also elucidate the full spectrum of mutations conferring resistance to asciminib (that appear not to be confined to the myristate binding pocket). Regular molecular response (MR) monitoring is fundamental for evaluating treatment efficacy, catching early signs of relapse, and intervening promptly in case of confirmed failure. Whenever MR is not deemed satisfactory according to the European LeukemiaNet or the National Comprehensive Cancer Network definitions, BCR::ABL1 KD mutations testing should be performed. When needed, prompt and informed TKI switch can improve response and outcome and prevent the accumulation of mutations, including highly challenging compound mutations. Novel technologies like next-generation sequencing and digital polymerase chain reaction have recently been explored for BCR::ABL1 KD mutation testing; they have both advantages and disadvantages that are discussed in this article. This review also provides suggestions for interpretation and clinical translation of mutation testing results, which may not always be straightforward, particularly in cases of low-level or unknown mutations.
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Affiliation(s)
- Simona Soverini
- Department of Medical and Surgical Sciences (DIMEC), Institute of Hematology “Lorenzo e Ariosto Seràgnoli,” University of Bologna, Bologna, Italy
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Kockerols C, Valk PJM, Blijlevens NMA, Cornelissen JJ, Dinmohamed AG, Geelen I, Hoogendoorn M, Janssen JJWM, Daenen LGM, Reijden BAVD, Westerweel PE. BCR::ABL1 kinase domain mutation testing and clinical outcome in a nationwide chronic myeloid leukemia patient population. Eur J Haematol 2023; 111:938-945. [PMID: 37731314 DOI: 10.1111/ejh.14107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 09/08/2023] [Accepted: 09/11/2023] [Indexed: 09/22/2023]
Abstract
OBJECTIVES Acquired missense mutations in the BCR::ABL1 kinase domain (KD) may cause tyrosine kinase inhibitor (TKI) treatment failure. Based on mutation-specific in vitro derived IC50-values, alternative TKI may be selected. We assessed clinical practice of BCR::ABL1 KD mutation testing, clinical response in relation to IC50-values, and clinical outcome of tested patients. METHODS Patients from six Dutch CML reference centers and a national registry were included once a mutational analysis was performed. Reasons for testing were categorized as suboptimal TKI response, and primary or secondary TKI resistance. RESULTS Four hundred twenty analyses were performed in 275 patients. Sixty-nine patients harbored at least one mutation. Most analyses were performed because of suboptimal TKI response but with low mutation incidence (4%), while most mutations were found in primary and secondary resistant patients (21% and 51%, respectively). Harboring a BCR::ABL1 mutation was associated with inferior overall survival (HR 3.2 [95% CI, 1.7-6.1; p < .001]). Clinically observed responses to TKI usually corresponded with the predicted TKI sensitivity based on the IC50-values, but a high IC50-value did not preclude a good clinical response per se. CONCLUSIONS We recommend BCR::ABL1 KD mutation testing in particular in the context of primary or secondary resistance. IC50-values can direct the TKI choice for CML patients, but clinical efficacy can be seen despite adverse in vitro resistance.
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MESH Headings
- Humans
- Fusion Proteins, bcr-abl/genetics
- Drug Resistance, Neoplasm/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/diagnosis
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Mutation
- Protein Kinase Inhibitors/therapeutic use
- Protein Kinase Inhibitors/pharmacology
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Affiliation(s)
- Camille Kockerols
- Department of Internal Medicine, Albert Schweitzer Hospital, Dordrecht, The Netherlands
| | - Peter J M Valk
- Department of Hematology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Nicole M A Blijlevens
- Department of Hematology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jan J Cornelissen
- Department of Hematology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Avinash G Dinmohamed
- Department of Research & Development, Netherlands Comprehensive Cancer Organisation (IKNL), Utrecht, The Netherlands
- Department of Public Health, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Hematology, Cancer Center Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
| | - Inge Geelen
- Department of Hematology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Mels Hoogendoorn
- Department of Hematology, Medical Center Leeuwarden, Leeuwarden, The Netherlands
| | - Jeroen J W M Janssen
- Department of Hematology, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Hematology, Amsterdam University Medical Center, location VUMC, Amsterdam, The Netherlands
| | - Laura G M Daenen
- Department of Hematology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Bert A van der Reijden
- Department of Laboratory Medicine, Lab of Hematology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Peter E Westerweel
- Department of Internal Medicine, Albert Schweitzer Hospital, Dordrecht, The Netherlands
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Cardinali D, Beldinanzi M, Ansuinelli M, Elia L, Della Starza I, Bellomarino V, Matarazzo M, Di Trani M, Cola M, Salutari P, Cedrone M, Bassan R, De Gobbi M, Della Porta MG, De Simone M, Alati C, Fracchiolla NS, Lunghi M, Intermesoli T, Cardinali V, Mulè A, Guarini A, Foà R, Chiaretti S. Digital droplet PCR for T315I BCR::ABL1 KD mutation assessment in adult Ph-positive acute lymphoblastic leukemia with a minimal residual disease increase. Leuk Lymphoma 2023; 64:1884-1887. [PMID: 37452789 DOI: 10.1080/10428194.2023.2235450] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/24/2023] [Accepted: 07/06/2023] [Indexed: 07/18/2023]
Affiliation(s)
- Deborah Cardinali
- Hematology, Department of Translational and Precision Medicine, "Sapienza" University of Rome, Rome, Italy
| | - Marco Beldinanzi
- Hematology, Department of Translational and Precision Medicine, "Sapienza" University of Rome, Rome, Italy
| | - Michela Ansuinelli
- Hematology, Department of Translational and Precision Medicine, "Sapienza" University of Rome, Rome, Italy
| | - Loredana Elia
- Hematology, Department of Translational and Precision Medicine, "Sapienza" University of Rome, Rome, Italy
| | - Irene Della Starza
- Hematology, Department of Translational and Precision Medicine, "Sapienza" University of Rome, Rome, Italy
- Fondazione GIMEMA Onlus, Rome, Italy
| | - Vittorio Bellomarino
- Hematology, Department of Translational and Precision Medicine, "Sapienza" University of Rome, Rome, Italy
| | - Mabel Matarazzo
- Hematology, Department of Translational and Precision Medicine, "Sapienza" University of Rome, Rome, Italy
| | - Mariangela Di Trani
- Hematology, Department of Translational and Precision Medicine, "Sapienza" University of Rome, Rome, Italy
| | - Mattia Cola
- Hematology, Department of Translational and Precision Medicine, "Sapienza" University of Rome, Rome, Italy
| | | | - Michele Cedrone
- UOC Ematologia, Ospedale San Giovanni Addolorata, Rome, Italy
| | - Renato Bassan
- Hematology Unit, Ospedale dell'Angelo and Ospedale Ss Giovanni e Paolo, Mestre Venezia, Italy
| | - Marco De Gobbi
- Department of Clinical and Biological Sciences, Haematopoietic Stem Cell Transplant Unit, University of Turin, San Luigi Gonzaga Hospital, Orbassano, Italy
| | | | | | - Caterina Alati
- Division of Hematology, Azienda Ospedaliera ''Bianchi Melacrino Morelli', Reggio Calabria, Italy
| | - Nicola Stefano Fracchiolla
- UOC Oncoematologia, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico di Milano, Università degli Studi di Milano, Milan, Italy
| | - Monia Lunghi
- Division of Hematology, Department of Translational Medicine, University of Eastern Piedmont, Novara, Italy
| | - Tamara Intermesoli
- Department of Oncology, Hematology University of Milan and Azienda Socio-Sanitaria Territoriale Papa Giovanni XXIII, Bergamo, Italy
| | - Valeria Cardinali
- Department of Medicine and Surgery, Institute of Hematology, Centro di Ricerca Emato-Oncologica (CREO), University of Perugia, Perugia, Italy
| | - Antonino Mulè
- UOC, Ospedali Riuniti, Villa Sofia-Cervello, Palermo, Italy
| | - Anna Guarini
- Hematology, Department of Translational and Precision Medicine, "Sapienza" University of Rome, Rome, Italy
| | - Robin Foà
- Hematology, Department of Translational and Precision Medicine, "Sapienza" University of Rome, Rome, Italy
| | - Sabina Chiaretti
- Hematology, Department of Translational and Precision Medicine, "Sapienza" University of Rome, Rome, Italy
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Cross NCP, Ernst T, Branford S, Cayuela JM, Deininger M, Fabarius A, Kim DDH, Machova Polakova K, Radich JP, Hehlmann R, Hochhaus A, Apperley JF, Soverini S. European LeukemiaNet laboratory recommendations for the diagnosis and management of chronic myeloid leukemia. Leukemia 2023; 37:2150-2167. [PMID: 37794101 PMCID: PMC10624636 DOI: 10.1038/s41375-023-02048-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 09/13/2023] [Accepted: 09/20/2023] [Indexed: 10/06/2023]
Abstract
From the laboratory perspective, effective management of patients with chronic myeloid leukemia (CML) requires accurate diagnosis, assessment of prognostic markers, sequential assessment of levels of residual disease and investigation of possible reasons for resistance, relapse or progression. Our scientific and clinical knowledge underpinning these requirements continues to evolve, as do laboratory methods and technologies. The European LeukemiaNet convened an expert panel to critically consider the current status of genetic laboratory approaches to help diagnose and manage CML patients. Our recommendations focus on current best practice and highlight the strengths and pitfalls of commonly used laboratory tests.
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Affiliation(s)
| | - Thomas Ernst
- Klinik für Innere Medizin II, Universitätsklinikum Jena, Jena, Germany
| | - Susan Branford
- Centre for Cancer Biology and SA Pathology, Adelaide, SA, Australia
| | - Jean-Michel Cayuela
- Laboratory of Hematology, University Hospital Saint-Louis, AP-HP and EA3518, Université Paris Cité, Paris, France
| | | | - Alice Fabarius
- III. Medizinische Klinik, Medizinische Fakultät Mannheim, Universität Heidelberg, Mannheim, Germany
| | - Dennis Dong Hwan Kim
- Department of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Canada
| | | | | | - Rüdiger Hehlmann
- III. Medizinische Klinik, Medizinische Fakultät Mannheim, Universität Heidelberg, Mannheim, Germany
- ELN Foundation, Weinheim, Germany
| | - Andreas Hochhaus
- Klinik für Innere Medizin II, Universitätsklinikum Jena, Jena, Germany
| | - Jane F Apperley
- Centre for Haematology, Imperial College London, London, UK
- Department of Clinical Haematology, Imperial College Healthcare NHS Trust, London, UK
| | - Simona Soverini
- Department of Medical and Surgical Sciences, Institute of Hematology "Lorenzo e Ariosto Seràgnoli", University of Bologna, Bologna, Italy
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Chen M, Xue J, Sang Y, Jiang W, He W, Hong S, Lv W, Xiao H, Liu R. Highly sensitive droplet digital PCR for detection of RET fusion in papillary thyroid cancer. BMC Cancer 2023; 23:363. [PMID: 37081420 PMCID: PMC10120194 DOI: 10.1186/s12885-023-10852-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 04/15/2023] [Indexed: 04/22/2023] Open
Abstract
BACKGROUND Thyroid cancer is the most frequent malignancy of the endocrine system, of which papillary thyroid cancer (PTC) is the predominant form with a rapid increasing incidence worldwide. Rearranged during transfection (RET) fusions are common genetic drivers of PTC and the potent RET inhibitor selpercatinib has been recently approved for treating advanced or metastatic RET fusion-positive thyroid cancer. In this study we aimed to develop a droplet digital PCR (ddPCR) system to accurately detect RET fusion in PTC samples. METHODS The frequency and distribution of RET fusions in PTC were analyzed using genomic data of 402 PTC patients in The Cancer Genome Atlas (TCGA) database. To establish the ddPCR system for detecting CCDC6::RET fusion, a plasmid containing CCDC6::RET infusion fragment was constructed as standard template, the annealing temperature and concentrations of primers and probe were optimized. The analytical performance of ddPCR and quantitative reverse transcription PCR (qRT-PCR) were assessed in standard templates and tissue samples from 112 PTC patients. Sanger sequencing was performed in all the RET fusion-positive samples identified by ddPCR. RESULTS RET fusions were observed in 25 (6.2%) of the 402 TCGA samples, and 15 (60%) of the RET fusion-positive patients had the CCDC6::RET fusion. Compared with qRT-PCR, the ddPCR method showed a lower limit of detection (128.0 and 430.7 copies/reaction for ddPCR and qRT-PCR, respectively). When applying the two methods to 112 tissue samples of PTC, eleven (9.8%) CCDC6::RET fusion-positive samples were detected by qRT-PCR, while ddPCR identified 4 additional positive samples (15/112, 13.4%). All the CCDC6::RET fusion-positive cases identified by ddPCR were confirmed by Sanger sequencing except for one case with 0.14 copies/uL of the fusion. CONCLUSION The accurate and sensitive ddPCR method reported here is powerful to detection CCDC6::RET fusion in PTC samples, application of this method would benefit more RET fusion-positive patients in the clinic.
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Affiliation(s)
- Mengke Chen
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-Sen University, No. 58, Zhongshan Second Road, Guangzhou, 510080, China
| | - Junyu Xue
- Department of Endocrinology, The First Affiliated Hospital, Sun Yat-Sen University, No. 58, Zhongshan Second Road, Guangzhou, 510080, China
| | - Ye Sang
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-Sen University, No. 58, Zhongshan Second Road, Guangzhou, 510080, China
| | - Wenting Jiang
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-Sen University, No. 58, Zhongshan Second Road, Guangzhou, 510080, China
| | - Weiman He
- Department of Endocrinology, The First Affiliated Hospital, Sun Yat-Sen University, No. 58, Zhongshan Second Road, Guangzhou, 510080, China
| | - Shubin Hong
- Department of Endocrinology, The First Affiliated Hospital, Sun Yat-Sen University, No. 58, Zhongshan Second Road, Guangzhou, 510080, China
| | - Weiming Lv
- Department of Breast and Thyroid Surgery, The First Affiliated Hospital, Sun Yat-Sen University, No. 58, Zhongshan Second Road, Guangzhou, 510080, China
| | - Haipeng Xiao
- Department of Endocrinology, The First Affiliated Hospital, Sun Yat-Sen University, No. 58, Zhongshan Second Road, Guangzhou, 510080, China.
| | - Rengyun Liu
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-Sen University, No. 58, Zhongshan Second Road, Guangzhou, 510080, China.
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Shin J, Jung C. Improving the Accuracy of Single-Nucleotide Variant Diagnosis Using On-Off Discriminating Primers. BIOSENSORS 2023; 13:380. [PMID: 36979592 PMCID: PMC10046569 DOI: 10.3390/bios13030380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 03/05/2023] [Accepted: 03/09/2023] [Indexed: 06/18/2023]
Abstract
Early detection of rare mutations through liquid biopsy can provide real-time information related to cancer diagnosis, prognosis, and treatment outcomes. Cell-free DNA samples used in liquid biopsies contain single-nucleotide variants (SNVs) with a variant allele frequency (VAF) of approximately ≤1%. Droplet digital polymerase chain reaction (ddPCR) is considered the gold standard of sequencing using liquid samples, generating amplicons from samples containing mutations with 0.001-0.005% VAF; however, it requires expensive equipment and time-consuming protocols. Therefore, various PCR methods for discriminating SNVs have been developed; nonetheless, non-specific amplification cannot be avoided even in the absence of mutations, which hampers the accurate diagnosis of SNVs. In this study, we introduce single-nucleotide variant on-off discrimination-PCR (Soo-PCR), a highly accurate and practical method that uses a 3'-end tailing primer for the on-off discrimination of low-abundance mutant-type targets, including SNVs. Soo-PCR minimizes the chance of incorrect judgments owing to its high discriminating power. Cancer markers, such as KRAS G12D, EGFR L858R, and EGFR T790M mutations, containing 0.1% VAF, were clearly detected in under 2 h with a high reliability comparable with that of ddPCR. This new method serves as a practical approach to accurately detect and evaluate low-abundance mutations in a user-friendly manner.
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9
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Su J, Zhang L, Lai L, Zhu W, Hu C. A Hemin-Graphene Nanocomposite-Based Aptasensor for Ultrasensitive Colorimetric Quantification of Leukaemia Cells Using Magnetic Enrichment. BIOSENSORS 2022; 12:bios12121070. [PMID: 36551037 PMCID: PMC9776134 DOI: 10.3390/bios12121070] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/18/2022] [Accepted: 11/20/2022] [Indexed: 05/31/2023]
Abstract
Diagnostic blood cell counting is of limited use in monitoring a minimal number of leukaemia cells, warranting further research to develop more sensitive and reliable techniques to identify leukaemia cells in circulation. In this work, a hemin-graphene nanocomposite-based aptasensor was developed for ultrasensitive colorimetric detection of leukaemia cells (CEM) using magnetic enrichment. Hemin-conjugated graphene oxide nanocomposites (HGNs) were prepared by hydrazine reduction using graphene oxide nanosheets and hemins. Hence, the prepared HGNs become able to absorb single-stranded DNA and acquire peroxidase-like activity. The aptamer sgc8c, which recognizes a specific target on leukaemia cells, was absorbed onto HGNs to capture the target CEM cancer cells. The captured target cells that associated with the HGNs were then concentrated and separated by magnetic beads (MBs) coated with sgc8c aptamers, forming a HGN-cell-MB sandwich structure. These sandwich structures can be quantified via an oxidation reaction catalysed by HGNs. By utilizing dual signal amplification effects generated by magnetic enrichment and the improved peroxidase activity of HGNs, the biosensor allowed for highly sensitive detection of 10 to 105 CEM cells with an ultra-low limit of detection (LOD) of 10 cells under optimal conditions. It is expected that the proposed aptasensor can be further employed in monitoring the minimal residual disease during the treatment of leukaemia.
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Affiliation(s)
- Jing Su
- School of Life Sciences, Jiangxi Science & Technology Normal University, Nanchang 330013, China
| | - Liqiang Zhang
- School of Life Sciences, Jiangxi Science & Technology Normal University, Nanchang 330013, China
| | - Luogen Lai
- School of Pharmacy, Jiangxi Science & Technology Normal University, Nanchang 330013, China
| | - Wufu Zhu
- School of Pharmacy, Jiangxi Science & Technology Normal University, Nanchang 330013, China
| | - Chong Hu
- School of Life Sciences, Jiangxi Science & Technology Normal University, Nanchang 330013, China
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